U.S. Department of Energy

Pacific Northwest National Laboratory

Jason McDermott

Jason McDermott
Professional Title: 
Scientist & Team Lead

Dr. Jason McDermott, senior research scientist, has extensive research experience in molecular and structural virology and data resource design, data integration and prediction of biological networks, bridging experimental and computational biology. Currently, his research interests include data integration of high-throughput ‘omics data for biomarker discovery, developing systems biology models in a number of systems focusing on host-pathogen interactions, characterizing phylogenetic and functional relationships in complex eukaryotic microbial communities, and using network inference and topology to characterize organism-level phenotypes. He is involved in the Center for Systems Biology of EnteroPathogens (http://sysbep.pnl.gov) and the Center for Systems Virology (http://www.systemsvirology.org).

  • Post-doctoral, University of Washington, Bioinformatics, 2006
  • Ph.D., Oregon Health & Science University, Structural Virology, 2000
  • B.A. Reed College, Biology, 1993
  • 1997 Sears Fellowship Award (OHSU)
  • 1998 Tartar Fellowship Award (OHSU)
  • 2008 Analytics Challenge Winner (Supercomputing 2008)
Research Interests: 
  • Systems biology
  • Network inference
  • Data integration
  • Biological networks
  • Machine learning


  • McDermott JE, M Partridge, and Y Bromberg. 2018. "Ten Simple Rules for Drawing Scientific Comics." PLoS Computational Biology 14(1):Article No. e1005845. doi:10.1371/journal.pcbi.1005845


  • McDermott JE. 2017. "Working Life: Drawing Connections." Science 356(6343):1202. doi:10.1126/science.356.6343.1202
  • Maier TV, M Lucio, LH Lee, N VerBerkmoes, CJ Brislawn, J Bernhardt, R Lamendella, JE McDermott, N Bergeron, SS Heinzmann, J Morton, A Gonzalez, G Ackermann, R Knight, K Riedel, R Krauss, P Schmitt-Kopplin, and JK Jansson. 2017. "Impact of Dietary Resistant Starch on the Human Gut Microbiome, Metaproteome and Metabolome." mBio 8(5):Article No. e01343-17.  doi:10.1128/mBio.01343-17
  • Wang J, Z Ma, SA Carr, P Mertins, H Zhang, Z Zhang, DW Chan, MJ Ellis, R Townsend, RD Smith, JE McDermott, X Chen, AG Paulovich, E Boja, M Mesri, C Kinsinger, H Rodriguez, KD Rodland, D Liebler, and B Zhang. 2017. "Proteome Profiling Outperforms Transcriptome Profiling for Coexpression Based Gene Function Prediction." Molecular & Cellular Proteomics. MCP 16(1):121-134.  doi:10.1074/mcp.M116.060301


  • McDermott JE, HD Mitchell, L Gralinski, AJ Eisfeld, L Josset, A Bankhead, G Neumann, SC Tilton, A Schafer, C Li, S Fan, SK Mcweeney, R Baric, MG Katze, and KM Waters. 2016. "The Effect of inhibition of PP1 and TNFa signaling on pathogenesis of SARS coronavirus." BMC Systems Biology 10(1):93.  doi:10.1186/s12918-016-0336-6
  • Bernstein HC, RS McClure, EA Hill, LM Markillie, WB Chrisler, MF Romine, JE McDermott, MC Posewitz, DA Bryant, A Konopka, JK Fredrickson, and AS Beliaev. 2016. "Unlocking the Constraints of Cyanobacterial Productivity: Acclimations Enabling Ultrafast Growth." mBio 7(4):Article No. e00949-16.  doi:10.1128/mBio.00949-16
  • McClure RS, CC Overall, JE McDermott, EA Hill, LM Markillie, LA McCue, RC Taylor, M Ludwig, DA Bryant, and AS Beliaev. 2016. "Network Analysis of Transcriptomics Expands Regulatory Landscapes in Synechococcus sp. PCC 7002." Nucleic Acids Research 44(18):8810-8825.  doi:10.1093/nar/gkw737
  • Mitchell HD, LM Markillie, WB Chrisler, MJ Gaffrey, D Hu, CJ Szymanski, Y Xie, ES Melby, A Dohnalkova, RC Taylor, EK Grate, SK Cooley, JE McDermott, A Heredia-Langner, and G Orr. 2016. "Cells Respond to Distinct Nanoparticle Properties with Multiple Strategies as Revealed by Single-Cell RNA-Seq." ACS Nano 10(11):10173-10185. doi:10.1021/acsnano.6b05452
  • Oxford KL, JP Wendler, JE McDermott, RA White, III, JD Powell, JM Jacobs, JN Adkins, and KM Waters. 2016. "The Landscape of Viral Proteomics and Its Potential to Impact Human Health." Expert Review of Proteomics 13(6):579-591.  doi:10.1080/14789450.2016.1184091
  • Shi T, M Niepel, JE McDermott, Y Gao, CD Nicora, WB Chrisler, LM Markillie, VA Petyuk, RD Smith, KD Rodland, P Sorger, W Qian, and HS Wiley. 2016. "Conservation of Protein Abundance Patterns Reveals the Regulatory Architecture of the of the EGFR-MAPK Pathway." Science Signaling 9(436):rs6.  doi:10.1126/scisignal.aaf0891
  • Tabb DL, X Wang, SA Carr, K Clauser, P Mertins, MC Chambers, JD Holman, J Wang, B Zhang, LJ Zimmerman, X Chen, H Gunawardena, S Davies, M Ellis, S Li, R Townsend, E Boja, K Ketchum, C Kinsinger, M Mesri, H Rodriguez, T Liu, S Kim, JE McDermott, SH Payne, VA Petyuk, KD Rodland, RD Smith, F Yang, DW Chan, B Zhang, H Zhang, Z Zhang, JY Zhou, and D Liebler. 2016. "Reproducibility of differential proteomic technologies in CPTAC fractionated xenografts." Journal of Proteome Research 15(3):691-706. doi:10.1021/acs.jproteome.5b00859
  • Zhang H, T Liu, Z Zhang, SH Payne, B Zhang, JE McDermott, JY Zhou, VA Petyuk, L Chen, D Ray, S Sun, F Yang, L Chen, J Wang, P Shah, SW Cha, P Aiyetan, S Woo, Y Tian, MA Gritsenko, TRW Clauss, C Choi, ME Monroe, SN Thomas, S Nie, C Wu, RJ Moore, KH Yu, DL Tabb, D Fenyo, V Bafna, Y Wang, H Rodriguez, E Boja, T Hiltket, R Rivers, LJ Sokoll, H Zhu, IM Shih, L Cope, A Pandey, B Zhang, M Snyder, D Levine, RD Smith, DW Chan, and KD Rodland. 2016. "Integrated proteogenomic characterization of human high grade serous ovarian cancer." Cell 166(3):755-765.  doi:10.1016/j.cell.2016.05.069


  • Li J, CC Overall, ES Nakayasu, AS Kidwai, MB Jones, R Johnson, NT Nguyen, JE McDermott, C Ansong, F Heffron, E Cambronne, and JN Adkins. 2015. "Analysis of the Salmonella regulatory network suggests involvement of SsrB and H-NS in sE-regulated SPI-2 gene expression." Frontiers in Microbiology 6:Artcle No. 27.  doi:10.3389/fmicb.2015.00027
  • Li J, CC Overall, R Johnson, MB Jones, JE McDermott, F Heffron, JN Adkins, and E Cambronne. 2015. "ChIP-Seq Analysis of the s E Regulon of Salmonella enterica Serovar Typhimurium Reveals New Genes Implicated in Heat Shock and Oxidative Stress Response." PLoS One 10(9):Article No. e0138466.  doi:10.1371/journal.pone.0138466
  • Li J, ES Nakayasu, CC Overall, R Johnson, AS Kidwai, JE McDermott, C Ansong, F Heffron, E Cambronne, and JN Adkins. 2015. "Global analysis of Salmonella alternative sigma factor E on protein translation." Journal of Proteome Research 14(4):1716-1726. doi:10.1021/pr5010423
  • Vartanian KB, HD Mitchell, S Stevens, VK Conrad, JE McDermott, and M Stenzel-Poore. 2015. "CpG preconditioning regulates miRNA expression that modulates genomic reprogramming associated with neuroprotection against ischemic injury." Journal of Cerebral Blood Flow and Metabolism 35(2):257-266.  doi:10.1038/jcbfm.2014.193
  • Webb-Robertson BJM, HK Wiberg, MM Matzke, JN Brown, J Wang, JE McDermott, RD Smith, KD Rodland, TO Metz, JG Pounds, and KM Waters. 2015. "Review, Evaluation, and Discussion of the Challenges of Missing Value Imputation for Mass Spectrometry-Based Label-Free Global Proteomics." Journal of Proteome Research 14(5):1993-2001. doi:10.1021/pr501138h


  • McDermott JE, Y Huang, B Zhang, H Xu, and Z Zhao. 2014. "Integrative Genomics and Computational Systems Medicine." BioMed Research International 2014:Article No. 945253. doi:10.1155/2014/945253
  • Aevermann B, BE Pickett, S Kumar, EB Klem, S Agnihothram, PS Askovich, A Bankhead, M Bolles, V Carter, JH Chang, TRW Clauss, P Dash, AH Diercks, AJ Eisfeld, AL Ellis, S Fan, MT Ferris, L Gralinski, R Green, MA Gritsenko, M Hatta, RA Heegel, JM Jacobs, S Jeng, L Josset, SM Kaiser, S Kelly, GL Law, C Li, J Li, C Long, ML Luna, MM Matzke, JE McDermott, V Menachery, TO Metz, HD Mitchell, ME Monroe, G Navarro, G Neumann, RL Podyminogin, SO Purvine, C Rosenberger, CJ Sanders, AA Schepmoes, AK Shukla, A Sims, P Sova, VC Tam, N Tchitchek, PG Thomas, SC Tilton, AL Totura, J Wang, BJM Webb-Robertson, J Wen, JM Weiss, F Yang, B Yount, Q Zhang, SK Mcweeney, RD Smith, KM Waters, Y Kawaoka, R Baric, A Aderem, MG Katze, and RH Scheuermann. 2014. "A Comprehensive Collection of Systems Biology Data Characterizing the Host Response to Viral Infection." Scientific Data 1:Article No. 140033.  doi:10.1038/sdata.2014.33
  • Kang SH, SH Kahan, JE McDermott, NS Flann, and I Shmulevich. 2014. "Biocellion: Accelerating Computer Simulation of Multicellular Biological System Models." Bioinformatics 30(21):3101-3108.  doi:10.1093/bioinformatics/btu498
  • Webb-Robertson BJM, MM Matzke, S Datta, SH Payne, J Kang, LM Bramer, CD Nicora, AK Shukla, TO Metz, KD Rodland, RD Smith, MF Tardiff, JE McDermott, JG Pounds, and KM Waters. 2014. "Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements." Molecular and Cellular Proteomics 13(12):3639-3646. doi:10.1074/mcp.M113.030932


  • Kim YM, B Schmidt, AS Kidwai, MB Jones, BL Deatherage, HM Brewer, HD Mitchell, BO Palsson, JE McDermott, F Heffron, RD Smith, SN Peterson, C Ansong, DR Hyduke, TO Metz, and JN Adkins. 2013. "Salmonella Modulates Metabolism During Growth under Conditions that Induce Expression of Virulence Genes." Molecular Biosystems 9(6):1522-1534. doi:10.1039/C3MB25598K
  • Ansong C, AC Rutledge, HD Mitchell, S Chauhan, MB Jones, YM Kim, K Mcateer, BL Deatherage, JL DuBois, HM Brewer, BC Frank, JE McDermott, TO Metz, SN Peterson, RD Smith, VL Motin, and JN Adkins. 2013. "A multi-omic systems approach to elucidating Yersinia virulence mechanisms." Molecular Biosystems 9(1):44-54.  doi:10.1039/C2MB25287B 
  • Hafen RP, LJ Gosink, JE McDermott, KD Rodland, K Kleese-Van Dam, and WS Cleveland. 2013. "Trelliscope: A System for Detailed Visualization in Analysis of Large Complex Data." In IEEE Symposium on Large-Scale Data Analysis and Visualization (LDAV 2013), October 13-14, 2013, Atlanta, Georgia, pp. 105-112.  IEEE, Piscataway, NJ. doi:10.1109/LDAV.2013.6675164
  • Matzke MM, JN Brown, MA Gritsenko, TO Metz, JG Pounds, KD Rodland, AK Shukla, RD Smith, KM Waters, JE McDermott, and BJM Webb-Robertson. 2013. "A Comparative Analysis of Computational Approaches to Relative Protein Quantification Using Peptide Peak Intensities in Label-free LC-MS Proteomics Experiments." Proteomics 13(3-4):493-503. doi:10.1002/pmic.201200269
  • McDermott JE, J Wang, HD Mitchell, BJM Webb-Robertson, RP Hafen, JA Ramey, II, and KD Rodland. 2013. "Challenges in Biomarker Discovery: Combining Expert Insights with Statistical Analysis of Complex Omics Data." Expert Opinion on Medical Diagnostics 7(1):37-51.  doi:10.1517/17530059.2012.718329
  • Mitchell HD, AJ Eisfeld, A Sims, JE McDermott, MM Matzke, BJM Webb-Robertson, SC Tilton, N Tchitchek, L Josset, C Li, AL Ellis, JH Chang, RA Heegel, ML Luna, AA Schepmoes, AK Shukla, TO Metz, G Neumann, A Benecke, RD Smith, R Baric, Y Kawaoka, MG Katze, and KM Waters. 2013. "A Network Integration Approach to Predict Conserved Regulators Related to Pathogenicity of Influenza and SARS-CoV Respiratory Viruses." PLoS One 8(7):e69374. doi:10.1371/journal.pone.0069374
  • Niemann G, RN Brown, IT Mushamiri, NT Nguyen, R Taiwo, A Stufkens, RD Smith, JN Adkins, JE McDermott, and F Heffron. 2013. "RNA Type III Secretion Signals that require Hfq." Journal of Bacteriology 195(10):2119-2125.  doi:10.1128/JB.00024-13
  • Sanfilippo AP, JN Haack, JE McDermott, SL Stevens, and M Stenzel-Poore. 2013. "Modeling Emergence in Neuroprotective Regulatory Networks." In Complex Sciences: Second International Conference COMPLEX 2012, December 5-7, 2012, Santa Fe, New Mexico. Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering, vol. 126, ed. K Glass, et al, pp. 291-302.  Springer, New York, NY.  doi:10.1007/978-3-319-03473-7_26
  • Wang J, BJM Webb-Robertson, MM Matzke, SM Varnum, JN Brown, RM Riensche, JN Adkins, JM Jacobs, JR Hoidal, MB Scholand, JG Pounds, MR Blackburn, KD Rodland, and JE McDermott. 2013. "A Semiautomated Framework for Integrating Expert Knowledge into Disease Marker Identification." Disease Markers 35(5):513-523.  doi:10.1155/2013/613529
  • Webb-Robertson BJM, MM Matzke, TO Metz, JE McDermott, J Walker, KD Rodland, JG Pounds, and KM Waters. 2013. "Sequential Projection Pursuit Principal Component Analysis - Dealing with Missing Data Associated with New -Omics Technologies." BioTechniques 54(3):165-168. 
  • Zhang B, Y Huang, JE McDermott, RH Posey, H Xu, and Z Zhao. 2013. "Interdisciplinary Dialogue for Education, Collaboration, and Innovation: Intelligent Biology and Medicine In and Beyond 2013." BMC Genomics 14(Suppl 8):Article No. S1.  doi:10.1186/1471-2164-14-S8-S1


  • McDermott JE, KB Vartanian, HD Mitchell, SL Stevens, AP Sanfilippo, and M Stenzel-Poore. 2012. "Identification and Validation of Ifit1 as an Important Innate Immune Bottleneck ." PLoS One 7(6):e36465.  doi:10.1371/journal.pone.0036465
  • Acquaah-Mensah G, D Malhotra, M Vulimiri, JE McDermott, and S Biswal. 2012. " Suppressed Expression of T-Box Transcription Factors is Involved in Senescence in Chronic Obstructive Pulmonary Disease." PLoS Computational Biology 8(7):e1002597. doi:10.1371/journal.pcbi.1002597
  • Archuleta MN, JE McDermott, JS Edwards, and H Resat. 2012. "An Adaptive Coarse Graining Method for Signal Transduction in Three-Dimensions." FUNDAMENTA INFORMATICAE 118(4):371-384.  doi:10.3233/FI-2012-720
  • Diamond DL, A Krasnoselski, KE Burnum, ME Monroe, BJM Webb-Robertson, JE McDermott, MM Yeh, JF Golib-Dzib, N Susnow, S Strom , S Proll, S Belisle, DE Purdy, A Rasmussen, KA Walters, JM Jacobs, MA Gritsenko, DG Camp, II, R Bhattacharya, JD Perkins, RL Carithers, IW Liou, AM Larson, A Benecke, KM Waters, RD Smith, and MG Katze. 2012. "Proteome and Computational Analyses Reveal New Insights into the Mechanisms of Hepatitis C Virus Mediated Liver Disease Posttransplantation." Hepatology 56(1):28-38. doi:10.1002/hep.25649
  • McDermott JE, DL Diamond, CD Corley, A Rasmussen, MG Katze, and KM Waters. 2012. "Topological Analysis of Protein Co-Abundance Networks Identifies Novel Host Targets Important for HCV Infection and Pathogenesis ." BMC Systems Biology 6(1):28. doi:10.1186/1752-0509-6-28
  • McDermott JE, KD Jarman, RC Taylor, MJ Lancaster, H Shankaran, KB Vartanian, SL Stevens, M Stenzel-Poore, and AP Sanfilippo. 2012. "Modeling Dynamic Regulatory Processes in Stroke." PLoS Computational Biology 8(10):e1002722.  doi:10.1371/journal.pcbi.1002722


  • McDermott JE, AL Corrigan, ES Peterson, CS Oehmen, G Niemann, E Cambronne, D Sharp, JN Adkins, R Samudrala, and F Heffron. 2011. "Computational prediction of type III and IV secreted effectors in Gram-negative bacteria ." Infection and Immunity 79(1):23-32. doi:10.1128/IAI.00537-10
  • McDermott JE, CS Oehmen, LA McCue, EA Hill, DM Choi, J Stockel, ML Liberton, HB Pakrasi, and LA Sherman. 2011. "A Model of Cyclic Transcriptomic Behavior in Cyanobacterium Cyanothece sp. ATCC 51142." Molecular Biosystems 7(8):2407-2418. doi:10.1039/C1MB05006K
  • McDermott JE, H Yoon, ES Nakayasu, TO Metz, DR Hyduke, AS Kidwai, BO Palsson, JN Adkins, and F Heffron. 2011. "Technologies and Approaches to Elucidate and Model the Virulence Program of Salmonella." Frontiers in Microbiology 2:121. doi:10.3389/fmicb.2011.00121
  • McDermott JE, MN Archuleta, BD Thrall, JN Adkins, and KM Waters. 2011. "Controlling the Response: Predictive Modeling of a Highly Central, Pathogen-Targeted Core Response Module in Macrophage Activation." PLoS One 6(2):e14673. doi:10.1371/journal.pone.0014673
  • McDermott JE, MN Costa, SL Stevens, M Stenzel-Poore, and AP Sanfilippo. 2011. "DEFINING THE PLAYERS IN HIGHER-ORDER NETWORKS: PREDICTIVE MODELING FOR REVERSE ENGINEERING FUNCTIONAL INFLUENCE NETWORKS." In Biocomputing 2011: Proceedings of the Pacific Symposium on Biocomputing, January 3-7, 2011, Kohala Coast, Hawaii, ed. RB Altman, et al, pp. 314-25.  World Scientific, London, United Kingdom.  doi:10.1142/9789814335058_0033
  • McDermott JE, P Braun, RA Bonneau, and DR Hyduke. 2011. "MODELING HOST-PATHOGEN INTERACTIONS: COMPUTATIONAL BIOLOGY AND BIOINFORMATICS FOR INFECTIOUS DISEASE RESEARCH (Session introduction)." In Pacific Syposium on Biocomputing 2012, January 3-7, 2012, Honolulu, Hawaii, vol. 17, pp. 283-286.  Stanford University, Stanford, CA. 
  • Aderem A, JN Adkins, C Ansong, J Galagan, S Kaiser, MJ Korth, GL Law, JE McDermott, S Proll, C Rosenberger, G Schoolnik, and MG Katze. 2011. "A Systems Biology Approach to Infectious Disease Research: Innovating the Pathogen-Host Research Paradigm." mBio 2(1):Article No. e00325.  doi:10.1128/mBio.00325-10
  • Heffron F, G Niemann, H Yoon, AS Kidwai, RN Brown, JE McDermott, RD Smith, and JN Adkins. 2011. "Salmonella-secreted Virulence Factors." Chapter 10 in Salmonella: From Genome to Function, ed. S Porwollik, pp. 187-223.  Caister Academic Press, Norfolk, United Kingdom. 
  • McDermott JE, H Shankaran, AJ Eisfeld, S Belisle, G Neumann, C Li, SK Mcweeney, CL Sabourin, Y Kawaoka, MG Katze, and KM Waters. 2011. "Conserved Host Response to Highly Pathogenic Avian Influenza Virus Infection in Human Cell Culture, Mouse and Macaque Model Systems." BMC Systems Biology 5:Article No. 190.  doi:10.1186/1752-0509-5-190
  • Niemann G, RN Brown, JK Gustin, A Stufkens, AS Shaikh-Kidwai, J Li, JE McDermott, HM Brewer, AA Schepmoes, RD Smith, JN Adkins, and F Heffron. 2011. "Discovery of Novel Secreted Virulence Factors from Salmonella enterica Serovar Typhimurium by Proteomic Analysis of Culture Supernatants." Infection and Immunity 79(1):33-43. doi:10.1128/IAI.00771-10
  • Rasmussen A, DL Diamond, JE McDermott, X Gao, TO Metz, MM Matzke, V Carter, S Belisle, MJ Korth, KM Waters, RD Smith, and MG Katze. 2011. "Systems Virology Identifies a Mitochondrial Fatty Acid Oxidation Enyzme, Dodecenoyl Coenzyme A Delta Isomerase, Required for Hepatitis C Virus Replication and Likely Pathogenesis." Journal of Virology 85(22):11646-11654.  doi:10.1128/JVI.05605-11
  • Taylor RC, AP Sanfilippo, JE McDermott, RL Baddeley, RM Riensche, RS Jensen, M Verhagen, and J Pustejovsky. 2011. "Enriching regulatory networks by bootstrap learning using optimised GO-based gene similarity and gene links mined from PubMed abstracts." International Journal of Computational Biology and Drug Design 4(1):56-82. doi:10.1504/IJCBDD.2011.038657
  • Yoon H, C Ansong, JE McDermott, MA Gritsenko, RD Smith, F Heffron, and JN Adkins. 2011. "Systems analysis of multiple regulator perturbations allows discovery of virulence factors in Salmonella ." BMC Systems Biology 5:Article No. 100.  doi:10.1186/1752-0509-5-100


  • McDermott JE, AP Sanfilippo, RC Taylor, RL Baddeley, RM Riensche, and RS Jensen. 2010. "An Integrated Approach to Predictive Genomic Analytics." In Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, pp. 390-393.  Association for Computing Machinery, New York, NY. doi:10.1145/1854776.1854837
  • Buchko GW, G Niemann, ES Baker, ME Belov, RD Smith, F Heffron, JN Adkins, and JE McDermott. 2010. "A multi-pronged search for a common structural motif in the secretion signal of Salmonella enterica serovar Typhimurium type III effector proteins." Molecular Biosystems 6(12):2448-2458.  doi:10.1039/c0mb00097c
  • Diamond DL, AJ Syder, JM Jacobs, CM Sorensen, KA Walters, S Proll, JE McDermott, MA Gritsenko, Q Zhang, R Zhao, TO Metz, DG Camp, II, KM Waters, RD Smith, CM Rice, and MG Katze. 2010. "Temporal Proteome and Lipidome Profiles Reveal HCV-Associated Reprogramming of Hepatocellular Metabolism and Bioenergetics ." PLoS Pathogens 6(1):Art. No. e1000719.  doi:10.1371/journal.ppat.1000719
  • Lawrence P, W Kittichotirat, JE McDermott, and RE Bumgarner. 2010. "A Three-way Comparative Genomic Analysis of Mannheimia haemolytica Isolates." BMC Genomics 11:535.  doi:10.1186/1471-2164-11-535
  • Lawrence P, W Kittichotirat, RE Bumgarner, JE McDermott, D Herndon, DP Knowles, and S Srikumaran. 2010. "Genome sequences of Mannheimia haemolytica serotype A2: ovine and bovine isolates." Journal of Bacteriology 192(4):1167-1168.  doi:10.1128/JB.01527-09
  • McDermott JE, MN Costa, DB Janszen, M Singhal, and SC Tilton. 2010. "Separating the Drivers from the Driven: Integrative Network and Pathway Approaches Aid Identification of Disease Biomarkers from High-Throughput Data." Disease Markers 28(4):253-266. 
  • Taylor RC, AP Sanfilippo, JE McDermott, RL Baddeley, RM Riensche, RS Jensen, and M Verhagen. 2010. "Learning Biological Networks via Bootstrapping with Optimized GO-based Gene Similarity." In Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, pp. 515-519.  Association for Computing Machinery, New York, NY.  doi:10.1145/1854776.1854875
  • Wang J, J Zhang, R Li, H Zheng, J Li, Y Zhang, H Li, P Ni, S Li, S Li, J Wang, D Liu, JE McDermott, R Samudrala, S Liu, J Wang, H Yang, J Yu, and GKS Wong. 2010. "Evolutionary transients in the rice transcriptome." Genomics, Proteomics & Bioinformatics 8(4):211-228. doi:10.1016/S1672-0229(10)60023-X


  • Cannon WR, BJM Webb-Robertson, AR Willse, M Singhal, LA McCue, JE McDermott, RC Taylor, KM Waters, and CS Oehmen. 2009. "An Integrative Computational Framework for Hypotheses-Driven Systems Biology Research in Proteomics and Genomics." Chapter 4 in Computational and Systems Biology: Methods and Applications, pp. 63-85.  Research Signpost, Trivandrum, India. 
  • McDermott JE, J Wang, J Yu, GKS Wong, and R Samudrala. 2009. "Prediction and Annotation of Plant Protein Interaction Networks." Chapter 9 in Plant Genomics and Bioinformatics, ed. GP Rao, C Wagner, RK Singh and ML Sharma, pp. 207-238.  Studium Press LLC, Houston, TX. 
  • McDermott JE, R Samudrala, RE Bumgarner, K Montogomery, and R Ireton. 2009. Computational Systems Biology.  Humana Press, Totowa, NJ. 
  • McDermott JE, RC Taylor, H Yoon, and F Heffron. 2009. "Bottlenecks and Hubs in Inferred Networks Are Important for Virulence in Salmonella typhimurium." Journal of Computational Biology 16(2):169-180.  doi:10.1089/cmb.2008.04TT
  • Frazier Z, JE McDermott, M Guerquin, and R Samudrala. 2009. "Computational representation of biological systems." Chapter 53 in Computational Systems Biology, Methods in Molecular Biology, vol. 541, pp. 535-550.  Humana Press, Totowa, NJ. 
  • Guerquin M, JE McDermott, Z Frazier, and R Samudrala. 2009. "The Bioverse API and Web Application." Chapter 22 in Computational Systems Biology, Methods in Molecular Biology, vol. 541, pp. 511-534.  Humana Press, Totowa, NJ. 
  • Rashid I, JE McDermott, and R Samudrala. 2009. "Inferring molecular interactions pathways from eQTL data." Chapter 10 in Computational Systems Biology, Methods in Molecular Biology, vol. 541, pp. 211-224.  Humana Press, Totowa, NJ. 
  • Samudrala R, F Heffron, and JE McDermott. 2009. "Accurate prediction of secreted substrates and identification of a conserved putative secretion signal for type III secretion systems." PLoS Pathogens 5(4):,
  • Sanfilippo AP, RL Baddeley, N Beagley, JE McDermott, RM Riensche, RC Taylor, and B Gopalan. 2009. "Using the Gene Ontology to Enrich Biological Pathways." International Journal of Computational Biology and Drug Design 2(3):221-235. doi:10.1504/IJCBDD.2009.030114
  • Shi L, C Ansong, HS Smallwood, LM Rommereim, JE McDermott, HM Brewer, AD Norbeck, RC Taylor, JK Gustin, F Heffron, RD Smith, and JN Adkins. 2009. "Proteome of Salmonella enterica serotype Tyhimurium Grown in Low Mg2+/pH Medium." Journal of Proteomics and Bioinformatics 2(9):388-397.  doi:10.4172/jpb.1000099
  • Shi L, C Ansong, HS Smallwood, LM Rommereim, JE McDermott, HM Brewer, AD Norbeck, RC Taylor, JK Gustin, F Heffron, RD Smith, and JN Adkins. 2009. "Proteome of Salmonella Enterica SerotypeTyphimurium Grown in a Low Mg2+/pH Medium." Journal of Proteomics and Bioinformatics 2(9):388-397.  doi:10.4172/jpb.1000099
  • Shi L, SM Chowdhury, HS Smallwood, H Yoon, HM Mottaz-Brewer, AD Norbeck, JE McDermott, TRW Clauss, F Heffron, RD Smith, and JN Adkins. 2009. "Proteomic Investigation of the Time Course Responses of RAW 264.7 Macrophages to Infection with Salmonella enterica." Infection and Immunity 77(8):3227-3233.  doi:10.1128/IAI.00063-09
  • Taylor RC, M Singhal, DS Daly, JM Gilmore, WR Cannon, KO Domico, AM White, DL Auberry, KJ Auberry, BS Hooker, GB Hurst, JE McDermott, WH McDonald, DA Pelletier, DA Schmoyer, and HS Wiley. 2009. "An analysis pipeline for the inference of protein-protein interaction networks." International Journal of Data Mining and Bioinformatics 3(4) (Sp. Iss. SI):409-430. 
  • Taylor RC, M Singhal, JB Weller, S Khoshnevis, L Shi, and JE McDermott. 2009. "A Network Inference Workflow Applied to Virulence-Related Processes in Salmonella typhimurium ." In Annals of the New York Academy of Sciences, vol. 1158, pp. 143-158.  PubMed, New York, NY. 
  • Toepel J, JE McDermott, T Summerfield, and LA Sherman. 2009. "Transcriptional analysis of the unicellular, diazotrophic cyanobacterium Cyanothece sp. ATCC 51142 grown under short day/night cycles." Journal of Phycology 45(3):610-620. 
  • Webb-Robertson BJM, LA McCue, N Beagley, JE McDermott, DS Wunschel, SM Varnum, JZ Hu, NG Isern, GW Buchko, K Mcateer, JG Pounds, SJ Skerret, D Liggitt, and CW Frevert. 2009. "A Bayesian Integration Model of High-Throughput Proteomics and Metabolomics Data for Improved Early Detection of Microbial Infections." In Pacific Symposium on Biocomputing, vol. 14, pp. 451-463.  World Scientific Publishing Co., Singapore, Singapore. 
  • Wichadakul D, JE McDermott, and R Samudrala. 2009. "Prediction and integration of regulatory and protein-protein interactions." Chapter 6 in Computational Systems Biology, Methods in Molecular Biology, vol. 541, pp. 101-144.  Humana Press, Totowa, NJ. 
  • Yoon H, JE McDermott, S Porwollik, M Mcclelland, and F Heffron. 2009. "Coordinated Regulation of Virulence during Systemic Infection of Salmonella enterica serovar Typhimurium." PLoS Pathogens 5(2):1-16. 


  • McDermott JE, and R Samudrala. 2008. "Bioinformatic characterization of plant networks." In Proceedings of the Asia Pacific Conference on Plant Tissue Culture and Agrobiotechnology (APaCPA) 2007.  Aimst University, Bedong, Malaysia. 
  • Ansong C, H Yoon, AD Norbeck, JK Gustin, JE McDermott, HM Mottaz, J Rue, JN Adkins, F Heffron, and RD Smith. 2008. "Proteomics Analysis of the Causative Agent of Typhoid Fever." Journal of Proteome Research 7(2):546-557.  doi:10.1021/pr070434u
  • Gorton I, CS Oehmen, and JE McDermott. 2008. "It Takes Glue to Tango: MeDICi integration framework creates data-intensive computing pipeline." Scientific Computing 25(7):16-24. 


  • Taylor RC, M Singhal, DS Daly, KO Domico, AM White, DL Auberry, KJ Auberry, BS Hooker, GB Hurst, JE McDermott, WH McDonald, DA Pelletier, DD Schmoyer, and WR Cannon. 2007. "SEBINI-CABIN: An Analysis Pipeline for Biological Network Inference, with a Case Study in Protein-Protein Interaction Network Reconstruction ." In Sixth International Conference on Machine Learning and Applications, (ICMLA 2007) , pp. 587-593.  IEEE Computer Society, Washington DC.  doi:10.1109/ICMLA.2007.63
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